The effect of SNCA 3' region on the levels of SNCA-112 splicing variant

Abstract

Genetic variability at the 3' region of SNCA locus has been repeatedly associated with susceptibility to sporadic Parkinson's disease (PD). Accumulated evidence emphasizes the importance of SNCA dosage and expression levels in PD pathogenesis. However, the mechanism through which the 3' region of SNCA gene modulates the risk to develop sporadic PD remained elusive. We studied the effect of PD risk-associated variants at SNCA 3' regions on SNCA112-mRNA (exon 5 in-frame skipping) levels in vivo in 117 neuropathologically normal, human brain frontal cortex samples. SNPs tagging the SNCA 3' showed significant effects on the relative levels of SNCA112-mRNA from total SNCA transcripts levels. The "risk" alleles were correlated with increased expression ratio of SNCA112-mRNA from total. We provide evidence for functional consequences of PD-associated SNCA gene variants at the 3' region, suggesting that genetic regulation of SNCA splicing plays an important role in the development of the disease. Further studies to determine the definite functional variant/s within SNCA 3'and to establish their association with PD pathology are necessary.

Fig. 1

A schematic representation of the human SNCA gene with the relative positions of the SNPs. Organization of the human SNCA locus: the alternative exon 5, wide white solid box; other translated exons, wide black solid boxes; 5′ and 3′UTR, narrow black solid boxes; introns and intergenic regions, gray line. The SNCA gene is in the minus strand, the 5′ and 3′ indicate the gene’s orientation. The gray arrow marks the transcription start site and direction. The relative positions of the genetic variants are indicated above; asterisks designate variants that were associated with ratio of SNCA112-mRNA

Fig. 2

Linkage disequilibrium (LD) structure of the 3′ region of SNCA gene. Genotypes of five SNPs from the sample set of this study (N=117) were used to determine LD (r²) within the SNCA 3′ region using Haploview software. r² values are shown within cells. Black cells, strong LD; shaded of gray cells, intermediate; white cells, evidence of recombination

Fig. 3

Effect of SNP genotypes at SNCA 3′ region on human SNCA112-mRNA expression levels relative to from total SNCA-mRNA levels in human frontal cortex. Individuals were genotyped for SNPs rs356219 (a), rs356165 (b), and rs2736990 (c). Fold levels of human SNCA112-mRNA in the frontal cortex were assayed by real-time RT–PCR using TaqMan technology and calculated relative the geometric mean of SYP and ENO mRNAs reference control using the 2^−ΔΔCt method (i.e., results presented are relative to a specific brain RNA sample). The values presented here are mean ratios from total SNCA-mRNA levels, adjusted for age, gender, ethnicity, PMI, and source. a Analysis of rs356219 showed that the risk allele G significantly correlates in an additive manner with higher ratio of SNCA112-mRNA levels (p= 0.009). b Analysis of rs356165 showed that the risk allele G significantly correlates in an additive manner with higher ratio of SNCA112-mRNA levels (p=0.01). c Analysis of rs2736990 showed that the risk allele G significantly correlates in an additive manner with higher ratio of SNCA112-mRNA levels (p=0.03)